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<linkHead>I) Getting started with PyTom</linkHead>
<ul>
  <li>
    <p><a href="./generalInfos.html" target="content">General information</a></p>
  </li>
  <li>
    <p><a href="./installation.html" target="content">Installation & Compile</a></p> 
  </li>
  <li>
    <p><a href="./genAPI.html" target="content">Generate API documentation</a></p> 
  </li>
  <li>
    <p><a href="./tutorialFiles.html" target="content">Get the tutorial files</a></p>
  </li>
  <li>
    <p><a href="./uiserver.html" target="content">Start UI Server</a></p>
  </li>
  <li>
    <p><a href="./faq.html" target="content">FAQ</a></p>
  </li>
</ul>
<linkHead>II) Workflow for subtomogram analysis</linkHead>
<ul>
  <li>
  <a href="./reconstructTomograms.html" target="content">Reconstruct a Tomogram from 
projections</a>
  </li>
  <li>
    <p>Localize particles automatically or interactively</p>
    <ul>
    <li>
      <p><a href="./localization.html" target="content">Localize Macromolecules automatically 
      (Template Matching)</a></p>
    </li>
    <li>
      <p><a href="./boxer.html" target="content">Pick particles interactively via EMAN2
      </a></p>
    </li>
    </ul>
  </li>
  <li>
  <a href="./reconstructSubtomograms.html" target="content">Reconstruct a batch of subtomograms 
from aligned and weighted projections</a>
  </li>
  <li>
  <p>Align and average Subtomograms</p>
    <ul>
      <li>
        <p><a href="./alignment.html" target="content">Align and average Subtomograms in real space</a></p>
      </li>
      <li>
        <p><a href="./frm.html" target="content">Align and average Subtomograms using 
	spherical harmonics (Fast rotational matching)</a></p>
      </li>
    </ul>
  </li>
  </li>
<li>
    <p>Classify Subtomograms</p>
    <ul>
      <li>
        <p><a href="./classification.html" target="content">Classify subtomograms using CPCA and MCO</a></p>
      </li>
      <li>
        <p><a href="./AC3D.html" target="content">Classify subtomograms using AC3D</a></p>
      </li>
    </ul>
  </li>
</ul>
<linkHead>III) Perform miscellaneous tasks</linkHead>
<ul>
  <li>
    <p><a href="./average.html" target="content">Create an average</a></p>
  </li>
  <li>
    <p><a href="./genMask.html" target="content">Generate a spherical mask</a></p>
  </li>
  <li>
    <p><a href="./cutParticles.html" target="content">Cut particles from a volume</a></p>
  </li>
  <li>
    <p><a href="./genParticleList.html" target="content">Generate a particle list from a directory</a></p>
  </li>
</ul>

<linkHead>IV) Data management</linkHead>
<ul>
  <li>
    <p><a href="./files.html" target="content">Files in PyTom</a></p>
  </li>
</ul>
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